{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2011/10/22/chembl-rdf-uploading-data-to-kasabi.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/k1860-kks41",
      "url": "https://chem-bla-ics.linkedchemistry.info/2011/10/22/chembl-rdf-uploading-data-to-kasabi.html",
      "title": "ChEMBL-RDF: Uploading data to Kasabi with pytassium",
      "content_html": "<p>I reported earlier how to I <a href=\"http://chem-bla-ics.blogspot.com/2011/07/chempedia-rdf-3-uploading-data-to.html\">uploaded the ChemPedia (RIP) data onto Kasabi</a>.\nBut for ChEMBL-RDF I have used the <a href=\"https://github.com/iand/pytassium\">pytassium</a> tool, not just because it has a cool name :) I discovered yesterday,\nhowever, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the\n<a href=\"http://kasabi.com/dataset/chembl-rdf\">ChEMBL-RDF data set on Kasabi</a>.</p>\n\n<p>The new triples I wanted to upload, link the <a href=\"http://chembl.blogspot.com/2011/08/chembl-11-released.html\">new public CHEMBL identifiers</a>\n(like <a href=\"https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL25\">CHEMBL25 for aspirin</a>) to the internal ChEMBL database identifier I used for\nChEMBL 09 for the URIs. So, I am adding a lot of triples like:</p>\n\n<div class=\"language-turtle highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"nl\">&lt;http://data.kasabi.com/dataset/chembl-rdf/09/molecule/m517180&gt;</span><span class=\"w\"> </span><span class=\"nl\">&lt;http://www.w3.org/2002/07/owl#sameAs&gt;</span><span class=\"w\">\n</span><span class=\"nl\">&lt;http://data.kasabi.com/dataset/chembl-rdf/09/chemblid/CHEMBL1&gt;</span><span class=\"w\">\n</span></code></pre></div></div>\n\n<p>And the pytassium code I use to upload this to Kasabi looks like:</p>\n\n<div class=\"language-python highlighter-rouge\"><div class=\"highlight\"><pre class=\"highlight\"><code><span class=\"kn\">import</span> <span class=\"n\">pytassium</span>\n<span class=\"kn\">import</span> <span class=\"n\">time</span>\n\n<span class=\"n\">dataset</span> <span class=\"o\">=</span> <span class=\"n\">pytassium</span><span class=\"p\">.</span><span class=\"nc\">Dataset</span><span class=\"p\">(</span><span class=\"sh\">'</span><span class=\"s\">chembl-rdf</span><span class=\"sh\">'</span><span class=\"p\">,</span><span class=\"sh\">'</span><span class=\"s\">XXX</span><span class=\"sh\">'</span><span class=\"p\">)</span>\n\n<span class=\"c1\"># Store the contents of a turtle file\n</span><span class=\"n\">dataset</span><span class=\"p\">.</span><span class=\"nf\">store_file</span><span class=\"p\">(</span><span class=\"sh\">'</span><span class=\"s\">chemblids.nt</span><span class=\"sh\">'</span><span class=\"p\">,</span> <span class=\"n\">media_type</span><span class=\"o\">=</span><span class=\"sh\">'</span><span class=\"s\">text/plain</span><span class=\"sh\">'</span><span class=\"p\">)</span>\n</code></pre></div></div>\n\n<p>So, that omission in my log book has been corrected now.</p>",
      "summary": "I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.",
      
      "date_published": "2011-10-22T00:00:00+00:00",
      "date_modified": "2011-10-22T00:00:00+00:00",
      "tags": ["kasabi","chembl","semweb"],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}